The evolution of methods for establishing evolutionary timescales

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 371, Issue 1699, 2016, Pages

  Donoghue, Philip C J ^a   Yang, Ziheng ^b  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Bayesian inference; Divergence times; Fossils; Molecular clock dating; Node calibrations; Tip calibrations

Indexed keywords

BAYESIAN ANALYSIS; CALIBRATION; DIVERGENCE; EVOLUTION; FOSSIL RECORD; GEOLOGICAL TIME; MOLECULAR ANALYSIS; PHYLOGENY; PROBABILITY; ROCK; SPECIES DIVERSITY;

ANATOMY AND HISTOLOGY; ANIMAL; CALIBRATION; CLASSIFICATION; EVOLUTION; FOSSIL; GENETIC PROCEDURES; MOLECULAR EVOLUTION; PALEONTOLOGY; PHYLOGENY; PROCEDURES; TIME; TRENDS;

ANIMALS; BIOLOGICAL EVOLUTION; CALIBRATION; CLASSIFICATION; EVOLUTION, MOLECULAR; FOSSILS; GENETIC TECHNIQUES; PALEONTOLOGY; PHYLOGENY; TIME;

EID: 84975297425     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2016.0020     Document Type: Review

References (103)

1. Pietsch TW. 2012 Trees of life: a visual history of evolution. Baltimore, MD: Johns Hopkins.
2. Bowler PJ. 1989 Evolution—the history of an idea. Berkeley, CA: University of California Press.
3. Lewis C. 2000 The dating game: one man‘s search for the age of the Earth. Cambridge, UK: Cambridge University Press.
4. Simpson GG. 1944 Tempo and mode in evolution. New York, NY: Columbia University Press.
5. Pearson PN, Ezard THG. 2013 Evolution and speciation in the Eocene planktonic foraminifer Turborotalia. Paleobiology 40, 130-143. (doi:10. 6084/m9.figshare.793840)
6. Wickström LM, Donoghue PCJ. 2005 Cladograms, phylogenies and the veracity of the conodont fossil record. Spec. Pap. Palaeontol. 73, 185-218.
7. Aze T, Ezard THG, Purvis A, Coxall HK, Stewart DRM, Wade BS, Pearson PN. 2011 A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data. Biol. Rev. 86, 900-927. (doi:10. 1111/j.1469-185X.2011.00178.x)
8. Lloyd GT, Pearson PN, Young JR, Smith AB. 2012 Sampling bias and the fossil record of planktonic foraminifera on land and in the deep sea. Paleobiology 38, 569-584. (doi:10.1666/11041.1)
9. Holland SM. 2016 The non-uniformity of fossil preservation. Phil. Trans. R. Soc. B 371, 20150130. (doi:10.1098/rstb.2015.0130)
10. Norell MA, Novacek MJ. 1992 The fossil record and evolution: comparing cladistic and paleontologic evidence for vertebrate history. Science 255, 1690-1693. (doi:10.1126/science.255.5052.1690)
11. Benton MJ, Wills MA, Hitchin R. 2000 Quality of the fossil record through time. Nature 403, 534-537. (doi:10.1038/35000558)
12. Nelson G. 1989 Species and taxa: systematics and evolution. In Speciation and its consequences (eds D Otte, JA Endler), pp. 60-81. Sunderland, MA: Sinauer.
13. Engelmann GF, Wiley EO. 1977 The place of ancestordescendant relationships in phylogeny reconstruction. Syst. Zool. 26, 1-11. (doi:10.2307/2412861)
14. Smith AB. 1994 Systematics and the fossil record: documenting evolutionary patterns. Oxford, UK: Blackwell Scientific.
15. Paul CRC. 1992 The recognition of ancestors. Hist. Biol. 6, 239-250. (doi:10.1080/10292389209380433)
16. Ronquist F, Klopfstein S, Vilhelmsen L, Schulmeister S, Murray DL, Rasnitsyn AP. 2012 A totalevidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Syst. Biol. 61, 973-999. (doi:10.1093/sysbio/sys058)
17. Foote M. 1996 On the probability of ancestors in the fossil record. Paleobiology 22, 141-151.
18. Bretsky SS. 1979 Recognition of ancestor-descendant relationships in invertebrate paleontology. In Phylogenetic analysis and paleontology (eds N Eldredge, J Cracraft), pp. 113-163. New York, NY: Columbia University Press.
19. Wagner PJ. 1998 Phylogenetic analysis and the quality of the fossil record. In The adequacy of the fossil record (eds SK Donovan, CRC Paul), pp. 165-187. Chichester, UK: John Wiley & Sons.
20. Paul CRC. 2003 Ghost ranges. In Telling the evolutionary time: molecular clocks and the fossil record (eds PCJ Donoghue, MP Smith), pp. 91-106. London, UK: Taylor & Francis.
21. Fisher DC. 1992 Stratigraphic parsimony. In MacClade version 3 Analaysis of phylogeny and character evolution (eds WP Maddison, DR Maddison), pp. 124-129. Sunderland, MA: Sinaeur Associates.
22. Wagner P. 1998 A likelihood approach for evaluating estimates of phylogenetic relationship among fossil taxa. Paleobiology 24, 430-449.
23. Forey PL. 2004 Systematics and paleontology. In Milestones in systematics (eds DM Williams, PL Forey), pp. 149-180. Boca Raton, FL: CRC Press.
24. Zuckerkandl E, Pauling L. 1965 Evolutionary divergence and convergence in proteins. In Evolving genes and proteins (eds V Bryson, HJ Vogel), pp. 97-166. New York, NY: Academic Press.
25. Zuckerkandl E, Pauling L. 1962 Molecular disease, evolution and genetic heterogeneity. In Horizons in biochemistry (eds M Kasha, B Pullman), pp. 189-225. New York, NY: Academic Press.
26. Wray GA, Levinton JS, Shapiro LH. 1996 Molecular evidence for deep precambrian divergences among metazoan phyla. Science 274, 568-573. (doi:10. 1126/science.274.5287.568)
27. Heckman DS, Geiser DM, Eidell BR, Stauffer RL, Kardos NL, Hedges SB. 2001 Molecular evidence for the early colonization of land by fungi and plants. Science 293, 1129-1133. (doi:10.1126/science.1061457)
28. Wikström N, Savolainen V, Chase MW. 2001 Evolution of the angiosperms: calibrating the family tree. Proc. R. Soc. Lond. B 268, 2211-2220. (doi:10. 1098/rspb.2001.1782)
29. Hedges SB, Parker PH, Sibley CG, Kumar S. 1996 Continental breakup and the ordinal diversification of birds and mammals. Nature 381, 226-229. (doi:10.1038/381226a0)
30. Runnegar B. 1982 A molecular-clock date for the origin of the animal phyla. Lethaia 15, 199-205. (doi:10.1111/j.1502-3931.1982.tb00645.x)
31. Brown RH, Richardson M, Boulter D, Ramshaw JAM, Jefferies RPS. 1972 The amino acid sequence of cytochrome c from Helix aspera Muëller (garden snail). Biochem. J. 128, 971-974. (doi:10.1042/bj1280971)
32. Donoghue PCJ, Smith MP. 2003 Telling the evolutionary time: molecular clocks and the fossil record. London, UK: CRC Press.
33. Jeram AJ, Selden PA, Edwards D. 1990 Land animals in the Silurian: arachnids and myriapods from Shropshire, England. Science 250, 658-661. (doi:10.1126/science.250.4981.658)
34. Kenrick P, Wellman CH, Schneider H, Edgecombe GD. 2012 A timeline for terrestrialization: consequences for the carbon cycle in the Palaeozoic. Phil. Trans. R. Soc. B 367, 519-536. (doi:10.1098/ rstb.2011.0271)
35. Sansom IJ, Smith MP, Smith MM. 1996 Scales of thelodont and shark-like fishes from the Ordovician. Nature 379, 628-630. (doi:10.1038/379628a0)
36. Andreev PS, Coates MI, Shelton RM, Cooper PR, Smith MP, Sansom IJ, Johanson Z. 2015 Upper Ordovician chondrichthyan-like scales from North America. Palaeontology 58, 691-704. (doi:10.1111/pala.12167)
37. Briggs DEG, McMahon S. 2015 The role of experiments in investigating the taphonomy of exceptional preservation. Palaeontology 59, 1-11. (doi:10.1111/pala.12219)
38. Holland SM. 1995 The stratigraphic distribution of fossils. Paleobiology 21, 92-109.
39. Patzkowsky ME, Holland SM. 2012 Stratigraphic paleobiology: understanding the distribution of fossil taxa in time and space. Chicago, IL: Chicago University Press.
40. Marshall CR. 1997 Confidence intervals on stratigraphic ranges with nonrandom distributions of fossil horizons. Paleobiology 23, 165-173.
41. Holland SM. 2000 The quality of the fossil record: a sequence stratigraphic perspective. Paleobiology 26, 148-168. (doi:10.1666/0094-8373(2000)26 [148:TQOTFR]2.0.CO;2)
42. Graur D, Martin W. 2004 Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet. 20, 80-86. (doi:10.1016/j.tig.2003.12.003)
43. Tamura K, Ursula Battistuzzi F, Billing-Ross P, Murillo O, Filipski A, Kumar S. 2012 Estimating divergence times in large molecular phylogenies. Proc. Natl Acad. Sci. USA 109, 19333-19338. (doi:10.1073/pnas.1213199109)
44. Kumar S, Hedges SB. 2016 Advances in time estimation methods for molecular data. Mol. Biol. Evol. 33, 863-869. (doi:10.1093/molbev/msw026)
45. Battistuzzi FU, Billing-Ross P, Murillo O, Filipski A, Kumar S. 2015 A protocol for diagnosing the effect of calibration priors on posterior time estimates: a case study for the Cambrian explosion of animal phyla. Mol. Biol. Evol. 32, 1907-1912. (doi:10. 1093/molbev/msv075)
46. Sanderson MJ. 1997 A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14, 1218-1231. (doi:10. 1093/oxfordjournals.molbev.a025731)
47. Yang Z, Yoder AD. 2003 Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species. Syst. Biol. 52, 705-716. (doi:10.1080/ 10635150390235557)
48. Thorne JL, Kishino H, Painter IS. 1998 Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15, 1647-1657. (doi:10. 1093/oxfordjournals.molbev.a025892)
49. Kishino H, Thorne JL, Bruno WJ. 2001 Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18, 352-361. (doi:10.1093/oxfordjournals. molbev.a003811)
50. Thorne JL, Kishino H. 2002 Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51, 689-702. (doi:10.1080/10635150 290102456)
51. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. 2006 Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88. (doi:10.1371/journal. pbio.0040088)
52. Yang Z, Rannala B. 2006 Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23, 212-226. (doi:10.1093/molbev/msj024)
53. Lartillot N, Lepage T, Blanquart S. 2009 PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25, 2286-2288. (doi:10.1093/bioinformatics/btp368)
54. Ronquist F et al. 2012 MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539-542. (doi:10.1093/sysbio/sys029)
55. Stadler T. 2010 Sampling-through-time in birth-death trees. J. Theoret. Biol. 267, 396-404. (doi:10. 1016/j.jtbi.2010.09.010)
56. Yang Z, Rannala B. 1997 Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 14, 717-724. (doi:10.1093/oxfordjournals.molbev.a025811)
57. Rannala B, Yang ZH. 2007 Inferring speciation times under an episodic molecular clock. Syst. Biol. 56, 453-466. (doi:10.1080/10635150701420643)
58. Dos Reis M, Yang Z. 2013 The unbearable uncertainty of Bayesian divergence time estimation. J. Syst. Evol. 51, 30-43. (doi:10.1111/j.1759-6831. 2012.00236.x)
59. O’Reilly J, dos Reis M, Donoghue PCJ. 2015 Dating tips for divergence time estimation. Trends Genet. 31, 637-650. (doi:10.1016/j.tig.2015.08.001)
60. Reisz RR, Muller J. 2004 Molecular timescales and the fossil record: a paleontological perspective. Trends Genet. 20, 237-241. (doi:10.1016/j.tig.2004.03.007)
61. Hedges SB, Kumar S. 2004 Precision of molecular time estimates. Trends Genet. 20, 242-247. (doi:10.1016/j.tig.2004.03.004)
62. Ho SYW, Phillips MJ. 2009 Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst. Biol. 58, 367-380. (doi:10.1093/sysbio/syp035)
63. Wilkinson RD, Steiper ME, Soligo C, Martin RD, Yang Z, Tavaré S. 2011 Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst. Biol. 60, 16-31. (doi:10. 1093/sysbio/syq054)
64. Warnock RCM, Yang Z, Donoghue PCJ. 2012 Exploring uncertainty in the calibration of the molecular clock. Biol. Lett. 8, 156-159. (doi:10. 1098/rsbl.2011.0710)
65. Warnock RCM, Parham JFJ, Joyce WG, Lyson TR, Donoghue PCJ. 2015 Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors. Proc. R. Soc. B 282, 20141013. (doi:10.1098/rspb.2014.1013)
66. Donoghue PCJ, Benton MJ. 2007 Rocks and clocks: calibrating the Tree of Life using fossils and molecules. Trends Ecol. Evol. 22, 424-431. (doi:10. 1016/j.tree.2007.05.005)
67. Müller J, Reisz RR. 2005 Four well-constrained calibration points from the vertebrate fossil record for molecular clock estimates. BioEssays 27, 1069-1075. (doi:10.1002/bies.20286)
68. Wang SC, Everson PJ. 2007 Confidence intervals for pulsed mass extinction events. Paleobiology 33, 324-336. (doi:10.1666/06056.1)
69. Wang SC, Everson PJ, Zhou HJ, Park D, Chudzicki DJ. 2016 Adaptive credible intervals on stratigraphic ranges when recovery potential is unknown. Paleobiology 42, 240-256. (doi:10.1017/pab.2015.37)
70. Donoghue PCJ, Smith MP, Sansom IJ. 2003 The origin and early evolution of chordates: molecular clocks and the fossil record. In Telling the evolutionary time: molecular clocks and the fossil record (eds PCJ Donoghue, MP Smith), pp. 190-223. London, UK: CRC Press.
71. Tavaré S, Marshall CR, Will O, Soligo C, Martin RD. 2002 Using the fossil record to estimate the age of the last common ancestor of extant primates. Nature 416, 726-729. (doi:10.1038/416726a)
72. Inoue JG, Donoghue PCJ, Yang Z. 2010 The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Syst. Biol. 59, 74-89. (doi:10.1093/sysbio/syp078)
73. Heath TA, Huelsenbeck JP, Stadler T. 2014 The fossilized birth–death process for coherent calibration of divergence-time estimates. Proc. Natl Acad. Sci. USA 111, E2957–E2966. (doi:10.1073/ pnas.1319091111)
74. Pyron RA. 2011 Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Syst. Biol. 60, 466-481. (doi:10. 1093/sysbio/syr047)
75. Lee MSY, Cau A, Naish D, Dyke GJ. 2014 Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds. Science 345, 562-566. (doi:10.1126/science.1252243)
76. Gorscak E, O’Connor PM. 2016 Time-calibrated models support congruency between Cretaceous continental rifting and titanosaurian evolutionary history. Biol. Lett. 12, 20151047. (doi:10.1098/rsbl.2015.1047)
77. Lee MS, Cau A, Naish D, Dyke GJ. 2014 Morphological clocks in paleontology, and a mid-Cretaceous origin of crown Aves. Syst. Biol. 63, 442-449. (doi:10.1093/sysbio/syt110)
78. Beck RMD, Lee MSY. 2014 Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals. Proc. R. Soc. B 281, 20141278. (doi:10.1098/rspb.2014.1278)
79. Donoghue MJ, Doyle J, Gauthier J, Kluge A, Rowe T. 1989 The importance of fossils in phylogeny reconstruction. Annu. Rev. Ecol. Syst. 20, 431-460. (doi:10.1146/annurev.es.20.110189.002243)
80. Gauthier J, Kluge AG, Rowe T. 1988 Amniote phylogeny and the importance of fossils. Cladistics 4, 105-209. (doi:10.1111/j.1096-0031.1988.tb00514.x)
81. Zhang C, Stadler T, Klopfstein S, Heath TA, Ronquist F. 2016 Total-evidence dating under the fossilized birth–death process. Syst. Biol. 65, 228-249. (doi:10.1093/sysbio/syv080)
82. Gavryushkina A, Heath TA, Ksepka DT, Stadler T, Welch D, Drummond AJ. 2015 Bayesian total evidence dating reveals the recent crown radiation of penguins. (http://arxiv.org/abs/ 1506.04797)
83. Sansom RS. 2015 Bias and sensitivity in the placement of fossil taxa resulting from interpretations of missing data. Syst. Biol. 64, 256-266. (doi:10.1093/sysbio/syu093)
84. Sansom RS, Wills MA. 2013 Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees. Sci. Rep. 3, 2545. (doi:10.1038/srep02545)
85. Sansom RS, Gabbott SE, Purnell MA. 2010 Nonrandom decay of chordate characters causes bias in fossil interpretation. Nature 463, 797-800. (doi:10. 1038/nature08745)
86. Jukes TH, Cantor CR. 1969 Evolution of protein molecules. In Mammalian protein metabolism (ed. HN Munro), pp. 21-132. New York, NY: Academic Press.
87. Condamine FL, Nagalingum NS, Marshall CR, Morlon H. 2015 Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating. BMC Evol. Biol. 15, 65. (doi:10.1186/s12862-015-0347-8)
88. Moore BR, Hohna S, May MR, Rannala B, Huelsenbeck JP. In press. Bayesian analysis of macroevolutionary mixtures: a critical appraisal. Proc. Natl Acad. Sci. USA.
89. May MR, Moore BR. In press. How well can we detect lineage-specific diversification-rate shifts? A simulation study of sequential AIC methods. Syst. Biol.
90. O’Reilly JE, Donoghue PCJ. 2016 Tips and nodes are complementary not competing approaches to the calibration of molecular clocks. Biol. Lett. 12, 20150975. (doi:10.1098/rsbl.2015.0975)
91. Lewis PO. 2001 A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50, 913-925. (doi:10.1080/ 106351501753462876)
92. Dos Reis M, Donoghue PC, Yang Z. 2015 Bayesian molecular clock dating of species divergences in the genomics era. Nat. Rev. Genet. 17, 71-80. (doi:10. 1038/nrg.2015.8)
93. Guillerme T, Cooper N. 2016 Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses. Biol. Lett. 12, 20151003. (doi:10.1098/rsbl.2015.1003)
94. Dembo M, Matzke NJ, Mooers AØ, Collard M. 2015 Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships. Proc. R. Soc. B 282, 20150943. (doi:10.1098/rspb.2015.0943)
95. Larson-Johnson K. 2015 Phylogenetic investigation of the complex evolutionary history of dispersal mode and diversification rates across living and fossil Fagales. New Phytol. 209, 418-435. (doi:10. 1111/nph.13570)
96. Fortey RA, Jefferies RPS. 1982 Fossils and phylogeny—a compromise approach. In Problems of phylogenetic reconstruction systematics association, vol. 21 (eds KA Joysey, AE Friday), pp. 197-234. London, UK: Academic Press.
97. Benton MJ. 1998 The quality of the fossil record of the vertebrates. In The adequacy of the fossil record (eds SK Donovan, CRC Paul), pp. 269-303. New York, NY: John Wiley & Sons.
98. Huelsenbeck JP, Rannala B. 1997 Maximum likelihood estimation of phylogeny using stratigraphic data. Paleobiology 23, 174-180.
99. Fisher DC. 2008 Stratocladistics: integrating temporal data and character data in phylogenetic inference. Annu. Rev. Ecol. Evol. Syst. 39, 365-385. (doi:10.1146/annurev.ecolsys.38.091206.095752)
100. Smith AB. 2000 Stratigraphy in phylogeny reconstruction. J. Paleontol. 74, 763-766. (doi:10. 1666/0022-3360(2000)074, 0763:SIPR.2.0.CO;2)
101. Fisher DC, Foote M, Fox DL, Leighton LR. 2002 Stratigraphy in phylogeny reconstruction— comment on Smith (2000). J. Paleontol. 76, 585-586. (doi:10.1666/0022-3360(2002)07 6, 0585:SIPRCO.2.0.CO;2)
102. Alroy J. 2002 Stratigraphy in phylogeny reconstruction—reply to Smith (2000). J. Paleontol. 76, 587-589. (doi:10.1666/0022-3360(2002) 076, 0587:SIPRRT.2.0.CO;2)
103. Wagner PJ. 2002 Testing phylogenetic hypotheses with stratigraphy and morphology—a comment on Smith (2000). J. Paleontol. 76, 590-593. (doi:10.1666/0022-3360(2002)076, 0590:TPHWSA.2.0.CO;2)